[gmx-users] how to add angle_restraints and dihedral_restraints for atoms belonging to two different molecules
mark.j.abraham at gmail.com
Sat May 18 10:43:25 CEST 2013
On Sat, May 18, 2013 at 10:20 AM, jnsong <jnsong at itcs.ecnu.edu.cn> wrote:
> Dear all,
> Recently, I want to add angle_restraints and dihedral_restraints for atoms
> in two separate molecules, that is, inter-molecular restraints, not
> intra-molecular restraints.
> I add the following into my .top file:
> [ angle_restraints ]
> ; i j k l type theta0 fc multiplicity
> 20 22 47 50 1 0.0 1500 1
> [ dihedral_restraints ]
> ; i j k l type label phi dphi kfac power
> 25 28 51 52 1 1 180 0 1 2
> But it give errors:
> "Fatal error:
> [ file ang_res.itp, line 5 ]:
> Atom index (47) in angle_restraints out of bounds (1-24).
> This probably means that you have inserted topology section
> in a part belonging to a different molecule than you intended to."
> Atom 20/22 belongs to one molecule, and Atom 47/50 belongs to another
> molecule. The same situation is for atom 25/28 and atom 51/52.
> I guess this error comes from the fact that I have two separate molecules
> in my simulation system, thus topol_Protein.itp and topol_Protein2.itp are
> produced when using pdb2gmx. Atom 47 in .gro file has atom number 17 in
> topol_Protein2.itp. Thus it gives the error that Atom index (47) in
> angle_restraints out of bounds!
> Additionally, [ angle_restraints] and [dihedral_restraints] seems for the
> intra-molecular interaction definitions.
> Would you please tell me how to add angle and dihedral restraints for the
> atoms that belong to two different molecules?
You need both molecules in the same [moleculetype], since the restraint
directives require this.
pdb2gmx -h will help here.
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